Genome-Wide Identification and Characterization of WOX Genes Regulating Somatic Embryogenesis in Catalpa bungei

Somatic embryogenesis (SE) is an indispensable biotechnological platform for plant regeneration, micropropagation and genetic modification. Members of WUSCHEL-related homeobox (WOX) transcription factor family are key regulators in SE, yet their roles in Catalpa bungei remain largely unexplored. C. bungei is a high-quality ornamental tree species endemic to China with prominent horticultural ornamental value. Here, we present the first genome-wide identification and expression profiling of the CbWOX gene family during SE in C. bungei. Fourteen CbWOX genes were identified and phylogenetically classified into three major clades. These genes are distributed across the 11 chromosomes of C. bungei, and their promoter regions are enriched with cis-regulatory elements associated with phytohormone response, stress adaptation, and growth/development. Integrated transcriptome and quantitative real-time PCR (qPCR) data indicated that CbWOX2, CbWOX5, CbWOX8, and CbWOX9 were highly expressed in embryogenic callus (EC), while CbWOX1.1 and CbWOX13 were predominantly expressed in non-embryogenic callus (NEC). Notably, only eight of the fourteen CbWOX genes were significantly expressed during SE, with distinct expression profiles across developmental stages. CbWOX4.1 and CbWOX4.2 were specifically associated with yellow-green hypocotyl callus development, while CbWOX2 and CbWOX8 were highly expressed at the EC stage. During later SE stages, CbWOX1.2, CbWUS, CbWOX5, and CbWOX13 showed significant expression at the globular embryo (GE) stage, while CbWOX1.3 was specifically upregulated at the cotyledon embryo (CE) stage. Our study provides a comprehensive genomic and transcriptomic foundation for the CbWOX family in C. bungei and reveals candidate genes with stage-specific expression during SE. These findings lay a solid basis for subsequent functional research to boost SE efficiency and advance the large-scale propagation of this precious ornamental tree.